Guake Indicator doesn't start automatically on login. To add it to startup, open Startup Applications, click "Add" and enter "guake-indicator" under "Name:" and "Command:", then click Add and you're done - Guake Indicator should now start automatically when you log in.

Guake Indicator should be available in the Debian repositories soon. Until then, you can try to use the Ubuntu packages in Debian (not tested).